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"Every object that biology studies is a system of systems." (Fran\c{c}ois Jacob, 1974). Most networks feature intricate architectures originating from tinkering, a repetitive use of existing components where structures are not invented but…
Learning and decision making in the brain are key processes critical to survival, and yet are processes implemented by non-ideal biological building blocks which can impose significant error. We explore quantitatively how the brain might…
Most social, technological and biological networks are embedded in a finite dimensional space, and the distance between two nodes influences the likelihood that they link to each other. Indeed, in social systems, the chance that two…
We present an analysis of the topologies of a class of networks which are optimal in terms of the requirements of having as short a route as possible between any two nodes while yet keeping the congestion in the network as low as possible.…
Biological networks have two modes. The first mode is static: a network is a passage on which something flows. The second mode is dynamic: a network is a pattern constructed by gluing functions of entities constituting the network. In this…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
Latent variable models for network data extract a summary of the relational structure underlying an observed network. The simplest possible models subdivide nodes of the network into clusters; the probability of a link between any two nodes…
Associative memory, traditionally modeled by Hopfield networks, enables the retrieval of previously stored patterns from partial or noisy cues. Yet, the local computational principles which are required to enable this function remain…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
We develop a framework to track the structure of temporal networks with a signal processing approach. The method is based on the duality between networks and signals using a multidimensional scaling technique. This enables a study of the…
Collaboration is a fundamental and essential characteristic of many complex systems, ranging from ant colonies to human societies. Each component within a complex system interacts with others, even at a distance, to accomplish a given task.…
A network is a typical expressive form of representing complex systems in terms of vertices and links, in which the pattern of interactions amongst components of the network is intricate. The network can be static that does not change over…
Although networks provide a powerful approach to study a large variety of ecological systems, their formulation does not typically account for multiple interaction types, interactions that vary in space and time, and interconnected systems…
A network representation is useful for describing the structure of a large variety of complex systems. However, most real and engineered systems have multiple subsystems and layers of connectivity, and the data produced by such systems is…
How does connectivity impact network dynamics? We address this question by linking network characteristics on two scales. On the global scale we consider the coherence of overall network dynamics. We show that such \emph{global coherence}…
Our work is motivated by and illustrated with application of association networks in computational biology, specifically in the context of gene/protein regulatory networks. Association networks represent systems of interacting elements,…
Modular structure is pervasive in many complex networks of interactions observed in natural, social and technological sciences. Its study sheds light on the relation between the structure and function of complex systems. Generally speaking,…
Physical networks are made of nodes and links that are physical objects embedded in a geometric space. Understanding how the mutual volume exclusion between these elements affects the structure and function of physical networks calls for a…
The properties of complex networked systems arise from the interplay between the dynamics of their elements and the underlying topology. Thus, to understand their behaviour, it is crucial to convene as much information as possible about…
In this paper, we consider the problem of exploring structural regularities of networks by dividing the nodes of a network into groups such that the members of each group have similar patterns of connections to other groups. Specifically,…